Showing posts with label Fungi. Show all posts
Showing posts with label Fungi. Show all posts

Tuesday, 27 August 2024

Oceanitis abyssalis: A new species of deep-sea wood-digesting Fungus from the Northwest Pacific abyssal plain.

The abyssal seafloor is an extreme environment, where organisms have to cope with high pressures, low oxygen and nutrient levels, permanent darkness, and low temperatures (with islands of extremely high temperatures around hydrothermal vents). Despite these obstacles, these deep-sea environments are home to a surprising range of organisms, including a number of Fungi which specialize in the decomposition of wood, a material of terrestrial origin. Do date only six species of obligate deepsea Fungi (i.e. Fungi found only in deep-sea environments) have been described, Alisea longicollaAllescheriella bathygenaBathyascus vermisporusOceanitis scuticellaPericonia abyssa, and Abyssomyces hydrozoicus, of which all except Abyssomyces hydrozoicus are wood-digesting species.

In a paper published in the journal Phytotaxa on 27 August 2024, Yukiro Nagano of the Marine Biodiversity and Environmental Assessment Research Center of the Japan Agency for Marine-Earth Science and Technology, and the Advanced Institute for Marine Ecosystem Change, Mohamed Adbul-Wahab of the Department of Botany and Microbiology at Sohag University, Ryota Nakajima, also of the Marine Biodiversity and Environmental Assessment Research Center of the Japan Agency for Marine-Earth Science and Technology, and Akinori Yabuki, also of the Advanced Institute for Marine Ecosystem Change, describe a new species of deep-sea wood-digesting Fungus from the Northwest Pacific abyssal plain.

The new species is placed in the genus Oceanitis on the basis of a genetic analysis, and given the specific name abyssalis in reference to the environment in which it was found, the abyssal plain of the Northwest  Pacific close to the Kuroshio Extension current boundary. The species is described on the basis of a colony found growing on a branch of wood with bark still attached, from a depth of 5707 m.

Oceanitis abyssalis (TNS-F-70722, holotype): Ascomata on wood. Nagano et al. (2024).

Oceanitis abyssalis produces fleshy yellowish or brownish ascomycota (spore-producing bodies) on the surface of the wood, which are yellowish in colour, 1.2-1.6 mm high and 0.98-1.2 mm in diameter. It is very similar, both morphologically and genetically, to samples of Oceanitis scuticella collected from the Kuril-Kamchatka Trench, but is morphologically different from the original description of Oceanitis scuticella, which was based upon material from bathyal depths near the islands of Vanuatu, which was not genetically analysed, and is no longer available (to date, no deep-sea Fungus has been cultured in the lab). For this reason, Nagano et al. question whether the Kuril-Kamchatka Trench Oceanitis scuticella material should be placed in this species, suggesting that Oceanitis cf abyssalis might be a better designation for the time being.  

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Saturday, 24 August 2024

Using microfossils and pollen to determine the origin of a set of stocks in the collection of the Rijksmuseum, Amsterdam.

In 2019 a man donated a set of stocks to the Rijksmuseum in Amsterdam, which he claimed his  grandfather had acquired in the  1970s from a farm in Zeeland Province.  The museum put the stocks on display in 2021, as part of an exhibition about the Dutch colony in Brazil between 1630 and 1654. In 2023, the stocks were loaned to the United Nations in New York, where they formed part of an exhibition about slavery in Dutch colonies. However, during the New York exhibition, questions were raised as to whether the stocks had ever actually been to South America. A radiocarbon analysis suggested that the tree from which the stocks had been made was probably felled in about 1800, with the stocks probably being made in the first quarter of the nineteenth century. Furthermore, DNA testing established that the wood came from a lineage of Oak trees, which today is found growing in Europe between northern Spain in in the south and southern Scandinavia in the north. 

In a paper published in the journal Review of Palaeobotany and Palynology on 10 August 2024, Hans Piena of the Vrije Universiteit Amsterdam, the Dutch Open Air Museum, and the Royal Netherlands Historical Society, Bas van Geel of the University of Amsterdam, Tom Hakbijl of the Naturalis Biodiversity Center, Arie Kalis of Goethe University, Pim van der Knaap and Jacqueline van Leeuwen, also of the University of Amsterdam, and Kees Nooren of Utrecht University, describe the results of a study which looked at palynological evidence (preserved pollen and spores) to develop a forensic picture of the environment in which the stocks had been used.

Oak stocks in the collection of the Rijksmuseum in Amsterdam (Inv.nr. NG.2019–502). Measurements: 265 × 37.5 × 23 cm. Piena et al. (2024).

Sediment was extracted from holes and cracks in the stocks, and analysed for palynomorphs (pollen, algae and spores), and the surface of the stocks were analysed for surface wear and other traces of use.

The stocks comprise two oak beams resting on a pair of cross-braces. Each beam has nine semicircular openings, which correspond to similar openings on the other beam, with the pair making a hole. on the other beam. At one end of the beams is an iron hinge, at the other an obliquely worn padlock eye. The insides of the holes have been smoothed to a shiny surface, suggesting that the stocks were used frequently. The upper surface of the beams are also smooth, having apparently been rubbed frequently with sand; cracks and small holes on this surface were filled with sediment. There are also a large number of chopping and cutting marks on the upper surface, in places forming a chequerboard pattern. The underside shows no signs of similar wear or sanding, and is largely free of sediment. 

The two cross-braces yielded traces of attacks by Fungi and Woodworm, which are not seen on the beams, and are interpreted by Piena et al. as feet upon which the stocks sat. They were previously interpreted as side braces in the two slavery exhibitions, which would have led to the stocks being horizontal, holding prisoners seated on the floor. Under Piena et al.'s interpretation, the holes would have been vertical, forcing anyone  trapped in the stocks to stand.

The number '22' has been written on the upper surface of the stocks in blue chalk. The fact that this has not been rubbed of strongly suggests that it was written after the stocks ceased being used, possibly as part of an inventory process or auction sale. Before the twentieth century, chalk could be produced in few colours other than white, but blue is one of those colours, making it possible the number was written in the nineteenth century. 

The contents of a sediment-filled hole on the upper surface of the stocks were analysed for siliceous microfossils. This produced about 500 000 Diatoms per gram of sediment, with fifty different species identified. These were largely indicative of a mesotrophic freshwater environment, such as a slow-flowing stream or ditch.  This included the epiphytic Diatom Cocconeis placentula, which grows on the surface of aquatic Plants or Macroalgae. No marine or brackish water species were found. Phytoliths (opaline silica crystals which build up in the leaves of Plants as dissolved monosillicic acid taken up with groundwater and precipitated out as water is lost from the leaves via transpiration) associated with Grasses were found, but none associated with Palms. Also present in great numbers were the stomatocysts of Chrysophytes (Golden-brown Algae), which are also typical of freshwater environments, with about 460 000 stomatocysts per gram of sediment. Also present were samples of the freshwater Alga Spirogyra and pollen of the freshwater Plant Myriophyllum alterniflorum. All of these species are indicative of freshwater ecosystems, but otherwise fairly cosmopolitan, and can be found in tropical and temperate environments.

Samples of pollen and spores were extracted from eight different cracks and holes on the surface of the stocks, with five samples being extracted from one large hole. A total of 7106 individual specimens were found, including 142 taxa of spores and pollen, from 18 trees, 21 shrubs, 91 herbs, 5 Ferns, and 7 types of Fungi, Algae, and Moss. This high proportion of herb pollen is likely to be indicative of an open agricultural environment, probably with low nutrient levels. This contained only a small proportion of Chenopodiaceaetype and Plantago maritima-type pollen, making a salt marsh environment unlikely. Many of the pollen types are cosmopolitan in distribution, but others, including Armeria, Cistaceae, Erica arborea, Lavandula, Nerium oleander, Olea, Pinus pinaster, Quercus ilex, Urtica pilulifera, Eryngium tenue, Corrigiola telephiifolia, and Vitis vinifera, are typical of the Mediterranean region, while others, including Erica australis, Erica umbellata, Cistus albidus, Cistus populifolius, Cistus ladanifer, and Halimium halimifolium, are found only on the western Iberian Peninsula and in western North Africa. Notably, the pollen of Cedrus and Chamaerops, which are more-or-less ubiquitous in recent North African sediments, were absent. 

Many pollen samples from cereal species showed signs of heat-deformation, something which has previously been observed in samples from medieval cesspits, and which is thought to be associated with bread or porridge-making.

The stocks also show signs of Insect damage in places, and yielded some Insect samples. The Insect damage comes in two forms. The first of these is wide flat tunnelling in the cambium layer, which would have underlain the bark, and which is caused by the larvae of Buprestid or Cerambycid Beetles. The second form of damage is a series of small boreholes likely to have been caused by Anobium punctatum, a small boring Beetle commonly associated with wooden beams and objects in Europe, which favours humid indoor environments. The Insect remains found belong to Ptinus fur or Ptinus clavipesAdistemia watsoniLatridius minutus, and two unidentified members of the Corticariinae. Adistemia watsoni is a species native to South America, but which had spread to Europe by the nineteenth century. The Spider Beetles, Ptinus fur and Ptinus clavipes, are typically found in indoor settings, feeding on Human food or other Pland and Animal remains. A small Mite belonging to the family Macrochelidae was also found. This assemblage has been found in other archaeological settings, and is considered typical of an indoor environment with mouldy food, litter and/or hay, and possibly excrement. 

The underside of one of the cross-braces, which is worn and shows traces of Fungal and Woodworm attack. Piena et al. (2024).

Artefacts will typically begin to assemble traces and small microparticles of biological origin from the moment when they are made, enabling researchers to build up a life history of  objects of interest. Examination of the assemblage associated with the Rijksmuseum stocks showed no evidence of these ever having visited South America, despite earlier interpretations.

A prior DNA analysis of the wood suggests that the stocks were made from a tree which probably grew somewhere between northern Spain and southern Scandinavia, and it seems unlikely that it was transported for any great distance before being worked. This is because only wood with a high market value is typically shipped for any great distance, which effectively means wood with a straight grain and few knots. The wood from which the stocks are made has an irregular grain pattern and is somewhat knotty, which would generally only be used if the desired task required wood to be sourced locally. The stocks also show signs of having been worked using techniques typical for green wood usage, which again makes it highly unlikely that the wood was transported any distance before being used.

The style of the stocks, with holes on top forcing the prisoner(s) to stand is unusual, but is known to have been used widely on the Iberian Peninsula during the early nineteenth century, leading Piena et al. to conclude that the stocks are likely to be of Iberian origin.

The samples collected can be expected to have started to accumulate as soon as the stocks were  made, and to have continued to accumulate throughout their existence. Samples were taken from locations all over the stocks, and in one in one location, a hole, a succession of samples were taken from different depths. Despite this, other than samples from the lower side being dusty and samples from the upper side being sandy, there was remarkably little difference in the samples, suggesting that the stocks spent much of their lives in a single environment. 

The pollen samples collected from the stocks suggest that this environment was in western Iberia, while the DNA collected from the wood suggests that it grew no  further south than northern Iberia, which is at least a neighbouring region. 

The Insects collected from the stocks suggest a humid, indoor environment, while the presence of cereal pollen, and good preservation of the Diatoms and pollen suggest that the sediment in which they were preserved did was not exposed to moisture for long periods.

Based upon this evidence, Piena et al. consider two separate scenarios, which could account for the accumulation of microfossils seen on the stocks. 

It is possible that the entire assemblage is post-use, representing a time when the stocks had been abandoned in a slow-moving stream or ditch, in an open agricultural environment with poor soils and intensive Rye cultivation, an environment typical of the Iberian Peninsula in the nineteenth century. This scenario is supported by the good preservation of pollen and Diatoms, the type of sediment found, and the low number of Fungal spores, but contradicted by the presence of sediment only on the upper side of the stocks, not on the underside or in the cavities between the beams and cross-braces. 

Alternatively, the large amount of pollen from wild Grasses and Cereals, particularly Rye, makes it possible that the stocks were used in an indoor environment where Grass and Rye straw were used as litter. This is supported by the types of spores present, which are all from species associated with decaying Plant matter or Animal dung (including Human). This is consistent with the idea that the stocks were used in a humid, indoor environment. The presence of Fungal and Woodworm damage to the underside of the stocks would be consistent with them sitting on a moist floor covered with a litter of straw and hay, possibly in a stable or dungeon (with the latter being more likely, given the presumed purpose of the stocks). Thus the deformed Cereal pollen could have come from bread or porridge fed to prisoners, or their faeces if they were forced to produce this while trapped in the stocks, and the sand in the cracks on the upper surface would be consistent with frequent scrubbing of this surface. 

Historically, most stocks around the world were positioned on their sides, with prisoners thus able to lie down. The Rijksmuseum stocks, however, are of a far rarer design, which held the prisoner in an upright position, forcing them to stand upright. Such stocks were often ued in conjunction with a neck brace on a wall, so that prisoners could be held upright and restrained. This was once common in Spanish prisons, providing a likely origin for the stocks. Notably, such stocks were particularly common during the Peninsula War of 1807-1814 and the Spanish War of Independence of 1814-1823, both wars which were noted for numerous attocities. In other settings, however, stocks of this type were combined with a latrine bench with holes, with prisoners being held in a sitting position.

Por liberal?, 1814–1823, by Francisco de Goya y Lucientes, showing a  woman trapped in a horizontal type of stocks. Piena et al. (2024).

When obtained, little was known about the set of stocks present in the collection of the Rijksmuseum. They were identified as having (recently) come from Zeeland, and were considered appropriate for an exhibition about the Dutch colony in Brazil between 1630 and 1658. Subsequent investigations have suggested that they were most likely made in Europe around 1800, and never taken to South America. Subsequent investigations by Piena et al. have narrowed the likely point of origin to the western Iberian Peninsula, and suggest that they were used in a moist indoor environment, most likely a dungeon.

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Thursday, 28 March 2024

Neotropicomus indicus: A 'South American' Mushroom from India.

The genus Neotropicomus was created in 2022 to include two species of Boletacean Mushrooms from South America, the previously described Xerocomus parvogracili (which became Neotropicomus parvogracili) from Guyana, and a new species, Neotropicomus australis, from the Atlantic Forests of Brazil. The name 'Neotropicomus' refers to the Neotropical Realm, the biological zone which incorporates the tropical biomes of South and Central America and the Caribbean islands, to which region the new genus was thought to be restricted.

In a paper published in the journal Cryptogamie Mycologie on 27 March 2024, Salna Nanu and Arun Kumar of the Department of Botany at the University of Calicut, describe a third species of Neotropicomus from Kerala State in India.

The new species is named Neotropicomus indicus, in reference to its unexpected presence in India. It produces small Mushrooms 20-30 mm across, which are convex when young, but flatten out as they age. The upper surfaces of the Mushrooms are reddish brown, fading to greyish towards the centre. The gills and stipe (stem) are white, with the stipe being 20-40 mm long and 3-4 mm wide.

Neotropicomus indicus, holotype, basidiomata. Nanu & Kumar (2024).

Neotropicomus indicus Mushrooms were found growing solitary in Diptocarp forests in Thiruvananthapuram District. It physically resembles other members of the genus Neotropicomus, and was confirmed as being the sister taxon to the other members of the genus by a genetic analysis.

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Wednesday, 20 March 2024

Zygosporium himachalensis: A fossil Ascomycote Fungus from the Miocene of Himachal Pradesh, India.

The genus Zygosporium contains asexual, largely saprotrophic, Ascomycete Fungi distinguished by dark brown setiform conidiophores (bristle-shaped spore producing bodies) with darkly pigmented, incurved, and swollen vesicles, often stacked, emerging either from the side of the conidiophore or from the mycelium (network of fungal threads).There are 22 described living species within the group, as well as three known fossil species, two from the Siwalik sediments of the eastern Himalayas, and one from the Oligocene of Hungary.

In a paper published in the journal Fungal Biology on 12 March 2023, Sampa Kundu and Mahasin Ali Khan of the Palaeobotany and Palynology Laboratory at the Department of Botany at Sidho-Kanho-Birsha University, describe a new species of Zygosporium from the Late Miocene Middle Siwalik of Himachal Pradesh, in the western Himalayas.

The new species is named Zygosporium himachalensis, where 'himachalensis' means 'from Himachal'. It is based upon a series of specimens found growing on a compressed Monocot leaf recovered from a grey mudstone in the Middle Siwalik in Mandi District of Himachal Pradesh. This location is about 8-10 km from, and probably coeval with Nalad Khad Section, which has been dated to 12-8 million years before the present.

(A) A compressed Monocot leaf segment; (B) Light microscopic image of Zygosporium himachalensis (SKBUH/PPL/HP/M40/S2) showing superficial or partly immersed hyphae with vesicular conidiophores in small or large groups or scattered on fossil Monocot leaf cuticle (SKBUH/PPL/HP/M40); (C), (D), (E), (G). Zygosporium himachalensis showing stacked chained vesicular cells on straight erect unbranched conidiophores; vesicular cells arising from apical, sub-apical, and lateral sides of the conidiophores (vesicular cells marked by blue arrows); (F) Zygosporium himachalensis showing stacked chained vesicular cells on a branched conidiophore (branching point marked by a black arrow; vesicular cells marked by blue arrows). Kundu & Khan (2024).

Specimens of Zygosporium himachalensis have erect, usually unbranched conidiophores, with chains of up to 4 integrated alternatively or suboppositely arranged vesicles arising directly from the mycelium. These are arranged in effuse or sometimes compact irregular-shaped patches on the surface of the leaf.

(A)–(L) Light microscopic images of Zygosporium himachalensis showing septate superficial conidiophore (marked by white arrows) with alternately (marked by blue arrows) and sub-oppositely (marked by green arrow) arranged dark brown to black, swollen, incurved, thick-walled vesicular cells (marked by red arrows); some vesicular cells with a cylindrical, brown, thick-walled, smooth, short stalk cell (marked by black arrows). Kunda & Khan (2024).

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Sunday, 3 March 2024

Talaromyces sedimenticola: A new species of Ascomycote Fungus from the deepest part of the Mariana Trench.

The Challenger Deep forms the deepest part of the Mariana Trench, reaching 10 971 m below sealevel. Curiously, recent studies have shown that the hadal depths of the oceans (areas more than 6 km deep) have a higher microbial carbon turnover than occurs at abyssal depths, between 4 km and 6 km below the surface. This has been supported by metagenomic studies which have shown significantly more genes coding for carbohydrate-active enzymes and peptidase are being expressed at these depths. This has led microbiologists to take an interest in the organisms living in the sediments of the deepest ocean trenches. 

In a paper published in the journal Antonie van Leeuwenhoek on 28 February 2024, Hongbo Zhou of the School of Minerals Processing and Bioengineering and the Key Laboratory of Biometallurgy at Central South University, Liting Xu and Wenxian Liu, also of the School of Minerals Processing and Bioengineering at Central South University, Kaiwen Ta of the Institute of Deep-Sea Science and Engineering of the Chinese Academy of Sciences, Xincun Wang of the State Key Laboratory of Mycology at the Institute of Microbiology of the Chinese Academy of Sciences, Jianwei Guo of the College of Agronomy and Life Sciences at Kunming University, Wenxi Luo, Zhiyuan Peng, and Qiaoni Huang, again of the School of Minerals Processing and Bioengineering at Central South University, and Yuguang Wang, once again of the School of Minerals Processing and Bioengineering and the Key Laboratory of Biometallurgy at Central South University, describe a new species of Ascomycote Fungi from the Challenger Deep.

The new species is described on the basis of two strains isolated from samples collected by the Research Vessel Tan Suo Yi Hao in September 2019, from a depth of 10 063 m below sealevel. A genetic analysis of these strains suggests that they belong to the same species, and, surprisingly, that that species  is a member of the genus Talaromyces, which mostly comprises terrestrial moulds, forming a sister taxon to a clade which includes Talaromyces trachyspermus, which is a serious commercial pest species, frequently infecting packaged fruit juices, and Talaromyces assiutensis, which is found growing within the leaves of Mangroves around the South China Sea. The new species is named Talaromyces sedimenticola, in reference to the environment where it was found.

Morphological characteristics of Talaromyces sedimenticola, (k), (l) conidiophores, (m) conidia. Zhou et al. (2024).

While morphologically similar, and genetically close, to other members of the genus TalaromycesTalaromyces sedimenticola shows some remarkable physiological traits, which mark it out as distinctive. It could be grown at temperatures of between 4°C and 50°C, unlike most Talaromyces species, which typically grow between about 28°C and 40°C. It could also survive and grow over a far wider pH range than any other species within the genus, pH 1.5-12, whereas other Talaromyces species could only survive in the pH range 4-8, with the exception of Talaromyces aculeatus, a widespread soil-dwelling form, which can survive over the range pH 1-7. Talaromyces sedimenticola is also remarkably halotollerant, able to flourish on media with 0-14% sodium chloride (weight over volume). More curiously, Talaromyces sedimenticola was unable to metabolise sucrose, tryptone, or monobasic potassium phosphate, all of which can be utilised by other members of the genus, although it was able to utilise other common foodstuffs, such as glucose, maltose, lactose, xylose, soluble starch, glycerol, peptone, ammonium sulphate, potassium phosphate, potassium chloride, and magnesium sulphate. 

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Tuesday, 30 January 2024

Tuber itzcuinzapotl: A new species of edible Truffle from Mexico.

Truffles, Tuber spp., are Ascomycote Fungi which from ectomycorrhizal relationships with a range of forest Plants, including Pines, Oaks, Hickories, and Orchids. They are distinguished for their large, tuber-like ascomata (fruiting bodies), which are formed underground, which often have highly distinctive aromas and flavours, leading to some species being traded as high-value gourmet items.

There are currently 25 species of Truffle known from Mexico, mostly from the temperate forests of the north and the mountains of the Neovolcanic axis. However, none of these are currently traded as foodstuffs, despite Mexico a globally leading countries in terms of the number of edible wild Fungi consumed, with about 500 species, making it second only China, where about 1000 are consumed. However, recent efforts have found that the non-native Black Truffle, Tuber melanosporum, will form ectomycorrhizal relationships with native Mexican Oaks, and several species found in Mexico are considered to have potential for commercial development, including the Pecan Truffle, Tuber lyonii, which is commercially exploited in the US and Canada, and can trade for up to US$400 per kg.

In a paper published in the journal Phytotaxa on 26 January 2024, Javier Isaac de la Fuente of the Colegio de Postgraduados at Campus Montecillo, Wendy Rosales-Rosales of the Instituto Tecnológico Superior de Zongolica of the Tecnológico Nacional de México, César Romero Martínez-González of the Instituto Tecnológico de Ciudad Victoria of the Tecnológico Nacional de México, Magdelana Martínez-Reyes, also of the Colegio de Postgraduados at Campus Montecillo, Andrea Carolina Elizondo-Salas, also of the Instituto Tecnológico Superior de Zongolica of the Tecnológico Nacional de México, and Jesús Pérez-Moreno, agian of the Colegio de Postgraduados at Campus Montecillo, describe a new species of edible Truffle from the Coniferous mixed forests of eastern Mexico.

The new species is named Tuber itzcuinzapotl, where 'itzcuinzapotl' means 'Dog's Zapote' in the Nahua language (a Zapote is a type of fruit). This Truffle produces subglobose fruiting bodies with a light brown, verrucous-granular outer surface, and an gray or pale brown interior, reaching up to 28 mm by 28 mm in size, with a distinctive fruity taste and smell. It is found growing in association with Mexcan Weeping Pines, Pinus patula, in Veracruz State, Mexico.

Tuber itzcuinzapotl (Holotype). Fresh ascomata fruiting body. De la Fuente et al. (2024).

Mexico has a significant culture of wild Fungus consumption, with over 500 types of Fungi consumed by members of all ethnic groups, and in particular rural communities living close to woodland. However, almost all consumed Fungi are epigeal, i.e, found above the ground, such as Mushrooms, with very little exploitation of subterranean species occurring. This is surprising, as Mexico is one of the most biodiverse regions in the world for Oaks, and Oaks are particularly associated with Fungi producing underground fruiting bodies. 

Tuber itzcuinzapotl is known to be consumed by members of the Nahua ethnic group living in the Sierra de Zongolica region of Veracruz State, Mexico, where it is referred to as 'itzcuinzapotl' (the specific name chosen for the species). Local folklore has it that people began to consume these Fungi after observing Dogs digging them up and eating them. Knowledge of the Fungus appeared to be restricted to older women in the community. Such local knowledge of wild foodstuffs is considered to be at risk in the region as traditional cultures are eroded, leading to loss of knowledge and a reduction and homogenisation in the number of foodstuffs consumed by Humans both in Mexico and globaly.

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